Has your Windows power management scheme got the ability to save energy on your USB ports after a period of inactivity? This setting is under the 'advanced' parameters of power options, accessed through your control panel.
What you're looking for is to see 'Disabled' present against the 'usb selective suspend setting'.
This is the starting point. If your difficulties persist afterwards then there could be other issues to check, but starting with the simplest possible cause is always a good policy.